All resequencing reads of the O. fragrans 161 accessions were mapped to the "Liuyejingui" reference genome ^[1]. SNP calling was performed using the Genome Analysis Toolkit (v4.1.4.1) ^[2]. The SNPs in the joint genotyping were further filtered to remove SNP sites with MAF < 0.05, sequencing depth < 4, and those that had samples with missing data. Finally, 2,022,974 high-quality variants were obtained, including 1,913,050 SNPs and 109,924 InDels. The large indels (> 50bp) in O. fragrans 161 accessions were identified using previous published software IndelEnsembler ^[3]. Totally, 818,412 large indels were obtained, including 322,517 deletions (DELs), 64,194 duplications (DUPs), and 431,701 insertions (INSs). The annotations and effects of SNPs on gene function were predicted using SnpEff (v5.0) software ^[4]. There are 163,725 variants in the gene coding sequences, 342 disruptive inframe InDels, and 2,829 variants caused potentially large effects such as stop codon gain or loss.

To explore the effect of variants on O. fragrans phenotypes, we developed the "Variation" module. The "Variation" module integrates genetic variation, and phenotype data, providing descriptions about the effect annotation, phenotype of genetic variations, and genotype-phenotype associations. In this module, users can enter the gene name, gene ID, or chromosome region to screen the candidate variations/genes for certain traits in the Single-locus or Multi-locus model.